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bio15anu / revelio

A lightweight utility for BS-seq and MethylC-seq data which applies a double-masking procedure on bisulfite alignments, facilitating variant calling with conventional software.
MIT License
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AttributeError: 'dict' object has no attribute 'to_dict' #2

Closed nelia89 closed 1 year ago

nelia89 commented 2 years ago

Hi, thank you so much for sharing this tool. I am very interested in using your script to get a masked.bam file to use it for subsequent variant calling analysis.

I already try the two different commands.

I obtained the calmd.bam output file when I run the samtools calmd -b command, but I did not obtain the masked.bam file.

And when I runned : ./revelio.py -f genome.fa input.bam masked.bam

I obtained this error:

Traceback (most recent call last): File "./revelio.py", line 445, in main(args.inbam,args.outbam,args.QUALITY,args.THREADS,args.temp,args.fasta) File "./revelio.py", line 94, in main header = original.header.to_dict() AttributeError: 'dict' object has no attribute 'to_dict'

Many thanks in advance for your help

bio15anu commented 1 year ago

Very sorry for the very late reply @nelia89, I somehow missed this issue! I hope you were able to solve it by yourself? It seems to me that you have not installed software dependencies prior to running Revelio, as to_dict() is a method from the pysam library. The error is stating that it does not recognise the method, which indicates that the library has not been loaded.

Please refer to the instructions on the landing page on Github for installing pysam with conda.